A schism is developing in northern Syria between jihadists and Free Syrian Army units, which threatens to pitch both groups against each other and open a new phase in the Syrian civil war.

Rebel commanders who fight under the Free Syrian Army banner say they have become increasingly angered by the behaviour of jihadist groups, especially the al-Qaida-aligned Jabhat al-Nusra, who they say aim to hijack the goals of the revolution.

The rising tensions are palpable in the countryside near Aleppo, which has become a stronghold for the well-armed and highly motivated jihadists, many of whom espouse the Bin Laden worldview and see Syria as a theatre in which to conduct a global jihad.

Syrian rebel groups, on the other hand, maintain that their goals are nationalistic and not aimed at imposing Islamic fundamentalism on the society if and when the Assad regime falls.

Fighting between the well-armed jihadists and the regular units who accepted their help from late last summer would mark a dramatic escalation in the conflict that has claimed in excess of 60,000 lives. However, commanders in the north say such an outcome now appears unavoidable.

"We will fight them on day two after Assad falls," one senior commander told the Guardian. "Until then we will no longer work with them."

In recent weeks Liwa al-Tawheed and other militias who form part of the overall Free Syrian Army brand have started conducting their own operations without inviting al-Nusra to join them.

A raid on an infantry school north of Aleppo in mid-December was one such occasion, as are ongoing attacks against Battalion 80 on the outskirts of the city's international airport and a military base to the east, known as Querres.

"They are not happy with us," the rebel commander said. "But they had been hoarding all their weapons anyway."

Another significant issue for rebel leaders is what to do with state assets that have now fallen into the hands of the opposition.

"They see stealing things that used to belong to the government, like copper factories, or any factory, as no problem," said the rebel commander. "They are selling it to the Turks and using the money for themselves. This is wrong. This is money for the people."

Jabhat al-Nusra does not eschew its links to al-Qaida, or the fact that many of its members are veterans of the insurgency against US forces in Iraq, which morphed into a sectarian war between Sunni and Shia Muslims.

In interviews, the group's members say they have learned lessons from Iraq, which saw them battered to the point of strategic defeat by a combination of a sustained push by US and Iraqi forces and a rebellion by Sunni communities against al-Qaida's pervasive and puritanical ways.

So far in Syria, al-Nusra has avoided targeting civilian facilities, or the country's minority communities. It has also started an outreach programme to communities ravaged by almost two years of war. The aid work has won the group some support in the north of the country, while also earning the ire of rebel groups.